An evil pilot named Morbulus who literally has an extra set of eyes on the back of his head is shot down into the bay by the SWAT Kats when he tries to destroy Megakat City’s oil refineries. He escapes and meets the half kat, half snake mad scientist Dr. Viper in the city sewers. Dr. Viper takes Morbulus back to his lab in the swamp and applies a drop of liquid to his arm, causing him to mutate into a “living test tube”; a huge, oozing bacterial monster. The bacteria then proceeds with Dr. Viper into the city via the sewer to break into Megakat Biochemical Labs. While rampaging through the city, it is discovered that the bacteria splits into separate entities if damaged or destroyed. The SWAT Kats suit up, and with the help of Callie Briggs and Dr. N. Zyme, prepare to stop the bacteria and Dr. Viper before they can cause any more harm.